Single-cell dynamics of antibiotic persistence reveal diverse modes of survival

Single cells of bacteria can exhibit phenotypic states that are tolerant to high doses of antibiotics without being resistant. Such persister cells are formed by stochastic switching and are typically present at low frequencies (as low as ~10^-6) in actively dividing populations. Due to their extremely low frequency, the mechanisms of persister formation at the single-cell level remain poorly understood. Using a novel, glass-etched microfluidic microchamber array capable of imaging ~10⁵ cells per experiment, we tracked over one million individual wild-type Escherichia coli cells before, during, and after antibiotic exposure. While previous studies have characterized dormant and slowly-growing persister cells that are formed in stationary phase, here we directly observe rapidly growing persister cells that are formed in exponential phase. Such persister cells display diverse survival behaviors, including continuous division, transient growth arrest, L-form-like morphology, and post-exposure filamentation. Moreover, we find that under ciprofloxacin treatment, all persisters – including those from stationary-phase cultures – correspond to cells that were actively growing prior to exposure. These results reveal history-dependent diversity in persistence dynamics at the single-cell level, which opens new directions for both quantitative modeling and biological understanding of bacterial persistence.